This list of frequently-asked questions (FAQs) about LexBIG is organized by subject and may include links to forum topics and other sources in addition to Knowledge Base articles. If you don't find an answer to your specific question, please email the VKC:Vocabulary Knowledge Centeror post a question in the LexBIG User forums.
Question: Can you explain the interaction with LexBIG?
Answer: LexBIG services are delivered as middleware.
- If the goal is to interact through a client program, refer to the Programmer Guide which can be found in the /doc folder of the installed materials.
- If the goal is to interact through a graphical user interface, options are available. The LexBIG GUI, as described in the programmer and administration guides, provides a basic API-centric way to query and visualize content. It is a development time tool written for audiences that are both technical and somewhat familiar with the LexBIG API.
- If the goal is to provide a general purpose end-user interface, other options are available. One browser-based front end to LexBIG is the National Center for Biomedical Ontology's (NCBO) BioPortal. Another is the National Cancer Institute's (NCI) Term Browser.
Question: What is "Coding Scheme Manifest"?
Answer: A "Coding Scheme Manifest" (or simply "manifest" as used interchangeably in this document) encapsulates the user-supplied values to set for a coding scheme while loading or converting an OWL (currently a manifest is supported only for OWL type of files) source to LexGrid format.
Question: What is "Coding Scheme"?
Answer: A Coding Scheme is the term that is used to represent an ontology/terminology being loaded or converted. In the LexGrid data model a terminology is represented as a coding scheme and it can reference other coding schemes. An example of coding scheme is "Amino Acid" which is described in the "amino-acid.owl" file.
A Coding Scheme has some meta information about it; values like 'formal name', 'local names', 'default language', 'version', 'copyright', 'sources' to name some.
Question: Why do we need a "Coding Scheme Manifest"?
Answer: When a terminology is being converted to the LexGrid data model from its native format (in this case OWL), Coding Scheme information is read from the source file. Sometimes values may be missing (not provided or invalid) or the author/user of the terminology wants to override or set default values despite (or in addition to) what is provided in the source file. This can be accomplished using "manifest" files along with the source file.
Question: Can I deploy LexBIG to operating systems other than Windows or Linux?
Answer: While you shouldn't need a separate installer, you will need to have the correct Java JDK installed for the system you are on. Some limitations will automatically apply. The GUI installer and a GUI browser may have problems with operating systems other than Windows or Linux. If the browser has options, note that we do have, in the package's Admin and Example folders, a fair amount of command line demonstration code that you might exercise.
Note that environments other than Windows or Linux are not tested or formally supported.
Question: Do I need to develop my own application client to create/update/search a concept and for imports/exports with LexBIG?
Answer: Searching can be accomplished by a graphical user interface or a general purpose end-user interface such as the NCI Term Browser. However, content creation and maintenance are considered out of scope for the current LexBIG API which addresses load, publish, and query of fully versioned ontologies. LexBIG can consume many types of file formats (e.g. XML, OBO, RRF, OWL) as versioned ontologies. Given any structured source, it should be possible to review these files and create a transform for load into the LexGrid repository.
Question: How are Vocabularies Loaded into LexBIG?
Answer: Content can be loaded using either the administrative functions provided by the LexBIG Graphical User Interface (GUI) or counterpart command-line scripts. Refer to the Installation and Administration Guide, which can be referenced in the /doc folder of the installed materials or is available as a document on this wiki page.
Question: What do I do when getting an error Connecting to MySQL?
Answer: LexBIG is distributed with an older version of the Java MySQL driver due to licensing concerns. If LexBIG reports an error concerning establishing a connection to the MySQL server yet the MySQL CLI is able to connect, a new version of Connector/J may be required. To update the driver, download the latest version from the MySQL site and place the mysql connector .jar file in the <install-root>/runtime/sqldrivers directory.
Also, be sure to rename or remove the older mm.mysql-2.0.6.jar to prevent any classpath issues.
The older jar file was sufficient to work with older mySQL environments, but has problems working with the latest MySQL 4.x and 5.x releases. Note that we cannot redistribute the latest driver due to license restrictions. It is likely that future LexBIG/LexEVS releases of the Java API will remove this older jar entirely, and require download as a separate step taken by the administrator as part of install.
Question: I am unable to find 'RELASE_INFO.RRF' that the install guide of the NCI Metathesaurus states is required for the load utility to work. Version 200803D does not have it - where do I find it?
The download location and reference to 'RELEASE_INFO.RRF' (also misspelled in the guide) are outdated and no longer correct.
Regarding the RELEASE_INFO file - notes dating to early 2006 indicate this file was a standard part of UMLS distributions and expected by the loader. It was not a standard part of the NCI RRF distribution, however, which is why it was noted in the guide. This file is no longer referenced or required by the NCI Meta loader. We recently loaded from versions without this file present as part of recent release testing (e.g. 200802D).
This information will be updated in documentation for future releases.
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